DreINT0046805 @ danRer10
Intron Retention
Gene
ENSDARG00000034307 | chrne
Description
cholinergic receptor, nicotinic, epsilon [Source:ZFIN;Acc:ZDB-GENE-040808-32]
Coordinates
chr5:37847121-37847531:-
Coord C1 exon
chr5:37847398-37847531
Coord A exon
chr5:37847166-37847397
Coord C2 exon
chr5:37847121-37847165
Length
232 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
AACTTTCCCTCCTTGAACAGAAT
3' ss Score
8.24
Exon sequences
Seq C1 exon
TCACTGGGAATGAAGAGTCACAGTTAATTGCTGATAAGTTTAAGAACTACAGTAAAAATATTCGACCAGCAAGACATGCAGATGAAAAAGTTAAGGTTCAGGTCAAGTTAACTCTCACCAACCTCATCTCCTTG
Seq A exon
GTAAGTAACCTTCATATTAACAGTGACAAGTTATTGTCAGTTTTAAACATATAAACATATATCTTTGCTAAAATATAACAAATAAAAATGTTCCAGAAAATTGTGTATCATTGATACTTTAATATAAAATATATGTGAGCAAATTATTTTGCTAATATTTATATATTTTTATTGATTTAGTGATTTATTTCATAGACTATTTGCATTCTGACAACTTTCCCTCCTTGAACAG
Seq C2 exon
AATGAAAAAGAAGAGACTTTAACTACAAATGTTTGGATTGAGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034307:ENSDART00000136428:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(18.0=86.7)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACTGGGAATGAAGAGTCACA
R:
TCCAAACATTTGTAGTTAAAGTCTCT
Band lengths:
171-403
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]